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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacattctaaccctaaccctaaccttttactcttctgtgttttgttagatgatatgtggttttggtgactggttctatttcttatgatatgtag

Basic information

species Arabidopsis thaliana
transcript AT5G35620.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G35620.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 5'ss of exon 2
------GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgta---ttacattctaacc----ctaaccctaaccttttactcttctgtgttttgt-tagatgatatgtggttttggtgactggttctatttcttatgatatgtag-----------------------
       |||||||||||||| ||||||||||| ||||| || || ||||||      ||  |   ||  ||||||    |  | || ||    ||||||||||| |||   || |  |  || |    || |   |   |     ||||   ||| ||||  || |  || ||| | ||     |     |  | ||  ||| || | |                         
TGTAGAACCAAAGTGGGAAGACCCAGAGTGTGCAAATGGGGGCAAATGGACT------GTGCCATGTAGCAGGAAGACCACCCTTGAGAACATGTGGCTTGAAACGgtacatttcctctaaaatcattgcttagtttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatcatttctgctgacaaacttttcgaacatgcag

upper sequence: AT5G35620.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G27570.1 (Glycine max), 5'ss of exon 2
GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacattctaaccctaaccctaaccttttactcttctgtgttttgttag-atgatatgtggttttggtgactggttctatttcttatgatatgtag
 || || ||||||||||||||||| || ||||||||||||||| ||         |        |||||||      | || ||    ||||||||||||||| |   || | |   |    ||      ||    ||  |||||| |  |  ||||  || | | | | ||  |  || |  || || |      |||
CCCTAAATGGGAAGATCCAGAGTGCGCCAATGGAGGAAAGTGGTCTATCACCAGCAACAGCGGCAGGAAGGCTAACCTTGATAACATGTGGCTTGAAACTgtaattgttttttagttttttgctggttggttttgttttcgtgtttagagaatatgaggtgagatct-gttgtttatttgtgattgttcttcggaatag

upper sequence: AT5G35620.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G21510.2 (Glycine max), 5'ss of exon 2
GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacattctaaccctaaccctaaccttttactcttctgtgttt------tgttagatgatatgtggttttggtgactggttctatttcttatgatatgtag
||| || ||||||||||| |||||||| ||||||||||||||| |          |        |||||||      | || ||    ||||||||||||||| |   || |     | || |  |    ||    ||  ||||||      | |  |  || || || ||||  |   |  || ||||||| |  |       
GCCTAAATGGGAAGATCCTGAGTGTGCCAATGGAGGAAAGTGGTCAGTCACCAGCAACAGCGGCAGGAAGGCTAACCTTGATAACATGTGGCTTGAAACTgtaattgtttttttgttttactccgattggttttcttttcgtgtttagagaatatggggagagatctgttttttattttttattgtatttctcaatag------

upper sequence: AT5G35620.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0049g01770.t01 (Vitis vinifera), 5'ss of exon 2
------GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacattctaaccctaaccctaaccttttactcttctgtgttttgttagatgatatgtggttttggtgactggttctatttcttatgatatgtag----------------------------
       ||||| ||||||||||| |||||||| |||||||| || ||||||      ||| |    |   | ||||    | | || |     ||||| ||||| |||  | ||   |||  |     ||   || |     |     | || || |  || ||| | | |||||   |  |    ||    ||   |   ||                            
GGTTGAACCAAAATGGGAAGATCCTGAGTGTGCAAATGGAGGCAAATGGACT------GTTGCCAGCAGCCGAAAGGGTAATCTTGATACCATGTGGCTAGAAACGgta--aaatgtgaactttgcatatagttttctggatctgacaatatttttgggagacatgagctgttggttcattttagagttgaacatatcagcaagttgataattgatgtgttttattgggtag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125197054|gb|EL212008.1|EL212008
EST:     TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGA
genomic: TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGA
EST: gi|125136084|gb|EL176114.1|EL176114
EST:     TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGATTGGAG
genomic: TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGATTGGAG
EST: gi|125058884|gb|EL127561.1|EL127561
EST:     AGCTTTAGACAAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGT
genomic: AGCTTTAGAC-AAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGT
EST: gi|116473054|gb|EG515646.1|EG515646
EST:     TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGT
genomic: TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGT
EST: gi|124815596|gb|EH900462.1|EH900462
EST:     TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGATTGGAGAGCAATTTGA
genomic: TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGA
EST: gi|125219842|gb|EL233927.1|EL233927
EST:     TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACT                         TTGATGGCTTTGAT
genomic: TTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacatt ... tgatatgtagTTGATGGCTTTGAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAAGTGGGAAGATCCAGAGTGTGCTAATGGAGGAAAGTGGACTTGGGTTGTTACTGCTAATAGGAAGGAAGCTTTAGACAAAGGCTGGCTTGAAACTgtattacattctaaccctaaccctaaccttttactcttctgtgttttgttagatgatatgtggttttggtgactggttctatttcttatgatatgtag

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